ArticleGenome research2001
Sequence-based design of single-copy genomic DNA probes for fluorescence in situ hybridization.
Article in Genome research, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 52 citations in OpenAlex.
- Cytogenetic screening of a Canadian swine breeding nucleus using a newly developed karyotyping method named oligo-banding.Genetics, selection, evolution : GSE · 2023Article
- Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights.BMC genomics · 2023Article
- Fluorescence in situ hybridization test for detection of endometrial carcinoma cells by non-invasive vaginal swab.Journal of cellular and molecular medicine · 2023Article
- Differentially accessible, single copy sequences form contiguous domains along metaphase chromosomes that are conserved among multiple tissues.Molecular cytogenetics · 2021Article
- PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments.Nature methods · 2021Article
- FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains.Frontiers in cell and developmental biology · 2021Review
- Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling.PLoS genetics · 2018Article
- OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Genotyping of KRAS Mutational Status by the In-Check Lab-on-Chip Platform.Sensors (Basel, Switzerland) · 2018Article
- Cytogenetic Diversity of Simple Sequences Repeats in Morphotypes of Brassica rapa ssp. chinensis.Frontiers in plant science · 2016Article
- Reversing chromatin accessibility differences that distinguish homologous mitotic metaphase chromosomes.Molecular cytogenetics · 2015Article
- Localized, non-random differences in chromatin accessibility between homologous metaphase chromosomes.Molecular cytogenetics · 2014Article
- Expanding probe repertoire and improving reproducibility in human genomic hybridization.Nucleic acids research · 2013Article
- Construction of repeat-free fluorescence in situ hybridization probes.Nucleic acids research · 2012Article
- Context-based FISH localization of genomic rearrangements within chromosome 15q11.2q13 duplicons.Molecular cytogenetics · 2011Article
- Distortion of quantitative genomic and expression hybridization by Cot-1 DNA: mitigation of this effect.Nucleic acids research · 2005Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromosomal rearrangements are frequently monitored by fluorescence in situ hybridization (FISH) using large, recombinant DNA probes consisting of contiguous genomic intervals that are often distant from disease loci. We developed smaller, targeted, single-copy probes directly from the human genome sequence. These single-copy FISH (scFISH) probes were designed by computational sequence analysis of approximately 100-kb genomic sequences. ScFISH probes are produced by long PCR, then purified, labeled, and hybridized individually or in combination to human chromosomes. Preannealing or blocking with unlabeled, repetitive DNA is unnecessary, as scFISH probes lack repetitive DNA sequences. The hybridization results are analogous to conventional FISH, except that shorter probes can be readily visualized. Combinations of probes from the same region gave single hybridization signals on metaphase chromosomes. ScFISH probes are produced directly from genomic DNA, and thus more quickly than by recombinant DNA techniques. We developed single-copy probes for three chromosomal regions-the CDC2L1 (chromosome 1p36), MAGEL2 (chromosome 15q11.2), and HIRA (chromosome 22q11.2) genes-and show their utility for FISH. The smallest probe tested was 2290 bp in length. To assess the potential utility of scFISH for high-resolution analysis, we determined chromosomal distributions of such probes. Single-copy intervals of this length or greater are separated by an average of 29.2 and 22.3 kb on chromosomes 21 and 22, respectively. This indicates that abnormalities seen on metaphase chromosomes could be characterized with scFISH probes at a resolution greater than previously possible.
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